Deeply buried water diversion tunnels frequently traverse regions with high seepage pressure and face numerous issues related to seepage. Therefore, implementing effective seepage control measures is critical. The main seepage control modes in modern tunnel engineering are the full blocking mode and the limited discharge mode. To investigate the impact of different seepage control modes on the seepage field, stress field, and displacement field and to reveal the synergistic seepage control effects among the tunnel’s structures under the limited discharge mode, this study conducts a model test using a self-developed three-dimensional hydro-mechanical coupling model testing system. Based on the engineering conditions of the Xiang-Lu Mountain tunnel, the test simulates tunnel excavation, support, and seepage drainage, successfully achieving the transition of seepage control mode from the full blocking mode to the limited discharge mode. For the tested conditions, the test results indicate that pre-excavation grouted reinforcement effectively mitigates the impact of excavation disturbances on the rock mass. The seepage pressure load on the lining in the limited discharge mode can decrease by up to 20%-25%. Grouted reinforcement and drainage holes effectively lower the seepage pressure load on the lining structure, although their influence on the seepage field diminishes with increasing distance from the tunnel. Under the limited discharge mode, a beneficial synergistic seepage control system is established within the tunnel, where the lining provides secondary support while the surrounding rock and grouted reinforcement area bear the primary load.